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José Luis Oliveira
Universidade de Aveiro, DETI / IEETA
3810-193 Aveiro, Portugal
jlo@ua.pt
(+351) 234 370 500
Author Archives: Rui Lebre
Eugene
EuGene is a gene redesign software. It allows opening and parsing genome files, loading genes into a workspace, and redesign the genes according to many redesign methodologies such as enhancing codon usage, codon context, GC content, hidden stop codons, repeated codons or nucleotides, harmonizing genes to other host species, avoiding deleterious sequences, among others. EuGene is free and auto-updates so you can always be up to the latest features and corrections.
Posted in Featured, Genomics, Software
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International School on SWAT4LS 2012 (May 2nd – 5th, Aveiro)
Registrations are now open! More information is available on the registration page.
The final deadline for registrations is April 24th
Posted in Front-Page News, News, Upcoming Events
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Talk (Helena Deus)
Helena Deus, “Linked Data and Semantic Web Technologies for improving discovery in the Life Sciences”
We live in a world of data. This is also true for the Life Sciences, where the introduction of omics technologies such as genome sequencing has led to the industrialization of data production beyond a craft-based cottage industry and into a […]
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GReEn
GReEn (Genome Resequencing Encoding) is a tool for compressing genome resequencing data using a reference genome sequence. It overcomes some drawbacks of the recently proposed tool GRS, namely, the possibility of compressing sequences that cannot be handled by GRS, faster running times and compression gains of over 100-fold for some sequences.
Posted in Featured, Genomics, Software
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Best PhD work in the Fraunhofer Portugal Challenge 2011
Daniel Polónia won the Fraunhofer Portugal Challenge 2011 in PhD category, with his work “Electronic marketplace for teleradiology services”, supervised by A Oliveira Duarte and José Luis Oliveira.
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III Workshop Ibero-NBIC – 2011
The III Workshop of the Iberoamerican network IBERO-NBIC, funded by the CYTED program, will be held in Aveiro, by October 10-11, 2011.
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Gimli
Gimli is an open source, high-performance and multi-corpus solution for automatic recognition of biomedical names. It uses Conditional Random Fields (CRFs) with a rich set of features, applying a method to combine different CRF models. Gimli achieves an F-measure of 87,54 on GENETAG and 73,05 on JNLPBA corpus, significantly outperforming existing open and closed source solutions.
Posted in Featured, Software, Text mining
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Totum
Totum is a innovative harmonisation solution for biomedical annotations, which uses Conditional Random Fields trained on several manually curated corpora. It avoids the single corpus dependency, supporting several biomedical domains and organisms. In the end, Totum harmonises annotations provided by several heterogeneous NER and normalisation solutions, following the gold standard requirements and guidelines.
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COEUS
Ipsa scientia potestas est. Knowledge itself is power.
Next-generation Semantic Web Application Framework.
Posted in Featured, Knowledge management, Software
Tagged api, coeus, framework, owl, rdf, semantic web, services, sparql, web
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XGB 2011 Best poster award
David Campos, Sérgio Matos, José Luis Oliveira, A machine learning-based tool for biomedical entity recognition, in III Xornada Galega de Bioinformática, Sep. 16, 2011, Vigo.
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WAVe
The Human Variome relates to genomic mutations and their effects on particular phenotypes. This critical life sciences research field has grown greatly in recent years, mostly due to the appearance of projects such as the Human Variome Project or the European GEN2PHEN Project. Nonetheless, locus-specific mutation databases and included variants are far from being standardized and widely used in the research community workflow.
Posted in Biomedical informatics, Featured, Software
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Talk (Daniel Sobral)
Daniel Sobral, “Ensembl Regulation”
Ensembl is a world reference for vertebrate genome annotation, providing high quality annotation for more than 50 species. Particularly challenging is the annotation of non-coding functional regions of the genome. Ensembl Regulation aims at making Ensembl
a reference for the annotation of genomic features with a potential role in the transcriptional regulation of gene expression. Combining publicly available […]
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PhD Defense (Daniel Polónia)
Daniel Polónia, “An electronic market for teleradiology services”
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PhD Defense (José Paulo Lousado)
José Paulo Lousado, “Pattern analysis on DNA primary structure”
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EU-ADR – Early Detection of Adverse Drug Events by Integrative Mining of Clinical Records and Biomedical Knowledge
Funding entity: FP7-ICT (STREP)
Period: 2008-2012
The overall objective of this project is the design, development and validation of a computerized system that exploits data from electronic healthcare records and biomedical databases for the early detection of adverse drug reactions.
An eHealth Successful Project
Posted in Past Projects, Projects
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GeNS
The Genomic Name Server is an innovative data integration system that incorporates a large set of heterogeneous biological data under a simple yet powerful schema. GeNS also addresses the cross-database low identifier coverage issue by proposing a new methodology of data integration.
Posted in Genomics, Software
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GeneBrowser
GeneBrowser is a web-based tool that, for a given list of genes, combines data from several public databases with visualisation and analysis methods to help identify the most relevant and common biological characteristics. The functionalities provided include the following: a central point with the most relevant biological information for each inserted gene; a list of the most related papers in PubMed and gene expression studies in ArrayExpress; and an extended approach to functional analysis applied to Gene Ontology, homologies, gene chromosomal localisation and pathways.
Posted in Biomedical informatics, Featured, Software
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Dicoogle
Dicoogle is an open-source Picture Archiving and Communications System (PACS) archive. Its modular architecture allows the quick development of new functionalities, due to the availability of a Software Development Kit (SDK).
Posted in Biomedical informatics, Featured, Software
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QuExT
QuExT (QUery EXpansion Tool) is designed to aid researchers find relationships between genes. It works through expanding each gene name into several associated terms and then querying a custom-designed PubMed index for scientific publications that refer to any of these terms.
Posted in Software, Text mining
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Neoscreen
NeoScreen is a bioinformatics software that helps diagnosis tasks in newborn screening programs. The application imports MS/MS raw data, and organizes and maintains all the information along the time in a database, providing a set of patterns that allow the detection of abnormalities in the blood samples. Is is been used, from 2005, to support the Portuguese Newborn Screning Program. Since May 2011, NeoScreen is represented by BMD Software Lda.
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